Representing Experiment Information in a MIAME Object

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Overview of MIAME Objects Constructing MIAME Objects Using Properties of a MIAME Object Using Methods of a MIAME Object

Overview of MIAME Objects

You can store information about experimental methods and conditions from a microarray gene expression experiment in a MIAME object. It loosely follows the Minimum Information About a Microarray Experiment (MIAME) specification. It can include information about:

• Experiment design

• Microarrays used

• Samples used

• Sample preparation and labeling

• Hybridization procedures and parameters

• Normalization controls

• Preprocessing information

• Data processing specifications

A MIAME object includes properties and methods that let you access, retrieve, and change experiment information related to a microarray experiment. These properties and methods are useful to view and analyze the information. For a list of the properties and methods, see MIAME class.

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Constructing MIAME Objects

For complete information on constructing MIAME objects, see MIAME class.

Constructing a MIAME Object from a GEO Structure

1. Import the bioma.data package so that the MIAME constructor function is available.

   import bioma.data.*
   

2. Use the getgeodata function to return a MATLAB structure containing Gene Expression Omnibus (GEO) Series data related to accession number GSE4616.

   geoStruct = getgeodata('GSE4616')
   
   geoStruct = 
   
       Header: [1x1 struct]
         Data: [12488x12 bioma.data.DataMatrix]

3. Use the MIAME constructor function to create a MIAME object from the structure.

   MIAMEObj1 = MIAME(geoStruct);

4. Display information about the MIAME object, MIAMEObj.

   MIAMEObj1 
   
   MIAMEObj1 = 
   
   Experiment Description:
     Author name: Mika,,Silvennoinen
   Riikka,,Kivelä
   Maarit,,Lehti
   Anna-Maria,,Touvras
   Jyrki,,Komulainen
   Veikko,,Vihko
   Heikki,,Kainulainen
     Laboratory: LIKES - Research Center
     Contact information: Mika,,Silvennoinen
     URL: 
     PubMedIDs: 17003243
     Abstract: A 90 word abstract is available. Use the Abstract property.
     Experiment Design: A 234 word summary is available. Use the ExptDesign property.
     Other notes: 
       [1x80 char]

Constructing a MIAME Object from Properties

1. Import the bioma.data package so that theMIAME constructor function is available.

   import bioma.data.*
   

2. Use the MIAME constructor function to create a MIAME object using individual properties.

   MIAMEObj2 = MIAME('investigator', 'Jane Researcher',...
                     'lab', 'One Bioinformatics Laboratory',...
                     'contact', 'jresearcher@lab.not.exist',...
                     'url', 'www.lab.not.exist',...
                     'title', 'Normal vs. Diseased Experiment',...
                     'abstract', 'Example of using expression data',...
                     'other', {'Notes:Created from a text file.'});

3. Display information about the MIAME object, MIAMEObj2.

   MIAMEObj2
   
   MIAMEObj2 = 
   
   Experiment Description:
     Author name: Jane Researcher
     Laboratory: One Bioinformatics Laboratory
     Contact information: jresearcher@lab.not.exist
     URL: www.lab.not.exist
     PubMedIDs: 
     Abstract: A 4 word abstract is available. Use the Abstract property.
     No experiment design summary available.
     Other notes: 
       'Notes:Created from a text file.'

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Using Properties of a MIAME Object

To access properties of a MIAME object, use the following syntax:

objectname.propertyname

For example, to retrieve the PubMed identifier of publications related to a MIAME object:

MIAMEObj1.PubMedID

ans =

17003243

To set properties of a MIAME object, use the following syntax:

objectname.propertyname = propertyvalue

For example, to set the Laboratory property of a MIAME object:

MIAMEObj1.Laboratory = 'XYZ Lab'

Note   Property names are case sensitive. For a list and description of all properties of a MIAME object, see MIAME class.

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Using Methods of a MIAME Object

To use methods of a MIAME object, use either of the following syntaxes:

objectname.methodname

or

methodname(objectname)

For example, to determine if a MIAME object is empty:

MIAMEObj1.isempty

ans =

     0

Note   For a complete list of methods of a MIAME object, see MIAME class.

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Representing Sample and Feature Metadata in MetaData Objects

Representing All Data and Information in an ExpressionSet Object

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